### Import libraries

import pathlib                  # file paths
import os                       # file paths
import warnings                 # warnings

import pandas as pd             # dataframes
import geopandas as gpd         # geodataframes
import numpy as np              # arrays
import xarray as xr             # multi-dimensional arrays
import rioxarray as rxr         # rasters + xarray
import rioxarray.merge as rxrm  # raster merging
import shapely                  # geometric operations
import time                     # time operations

import geoviews as gv           # geospatial visualizations
import holoviews as hv          # interactive visualizations
import hvplot.pandas            # pandas visualizations
import hvplot.xarray            # xarray visualizations
from cartopy import crs as ccrs # coordinate reference systems

import matplotlib               # plotting
import matplotlib.pyplot as plt # plotting
import scipy.stats as stats     # statistical analysis

import pystac_client            # STAC catalog access
from sodapy import Socrata      # Socrata Open Data API
import requests                 # JSON Census API requests

from tqdm.notebook import tqdm      # progress bars
from scipy.ndimage import convolve  # image processing
from scipy.ndimage import label     # image processing
from bokeh.models import NumeralTickFormatter  # plot formatting

from sklearn.linear_model import LinearRegression           # linear regression model
from sklearn.model_selection import train_test_split        # train-test split
from sklearn.model_selection import KFold                   # k-fold cross-validation
from sklearn.metrics import mean_squared_error, r2_score    # model evaluation metrics

### Create reproducible file paths
dir = os.path.join(
    pathlib.Path.home(),

    'Data',
    'Earth Analytics',
    'greenspace-portfolio'

)

os.makedirs(dir, exist_ok=True)

### Prevent GDAL from quitting due to momentary disruptions
os.environ["GDAL_HTTP_MAX_RETRY"] = "5"
os.environ["GDAL_HTTP_RETRY_DELAY"] = "1"

### Set up the census tract path

tract_dir = os.path.join(dir, 'chicago-tract')
os.makedirs(tract_dir, exist_ok=True)
tract_path = os.path.join(tract_dir, 'chicago-tracts.shp')

### Download the census tracts (only once)
if not os.path.exists(tract_path):
    tract_url = ('https://data.cdc.gov/download/x7zy-2xmx/application%2Fzip')

    tract_gdf = gpd.read_file(tract_url)

    chi_tract_gdf = tract_gdf[tract_gdf.PlaceName == 'Chicago']

    chi_tract_gdf.to_file(tract_path, index = False)

### Load in census tract data

chi_tract_gdf = gpd.read_file(tract_path)
chi_tract_gdf

### Site plot -- Census tracts with satellite imagery in the background
(
    chi_tract_gdf

    .to_crs(ccrs.Mercator())

    .hvplot(
        line_color = 'blue', fill_color = None,
        crs = ccrs.Mercator(), tiles = 'EsriImagery',
        frame_width = 600,
        title = 'Chicago Census Tracts'
    )
)

chi_tract_gdf

### Set up a path for the asthma data
cdc_path = os.path.join(dir, 'asthma.csv')

### Download asthma data (only once)
if not os.path.exists(cdc_path):
    cdc_url = (
        'https://data.cdc.gov/resource/cwsq-ngmh.csv'
        "?year=2023"
        "&stateabbr=IL"
        "&countyname=Cook"
        "&measureid=CASTHMA"
        "&$limit=1500"
    )

    cdc_df = (
        pd.read_csv(cdc_url)

        .rename(columns = {
            'data_value': 'asthma',
            'low_confidence_limit': 'asthma_ci_low',
            'high_confidence_limit': 'asthma_ci_high',
            'locationname': 'tract'})

        [[
            'year','tract', 'asthma',
            'asthma_ci_low', 'asthma_ci_high', 'data_value_unit', 
            'totalpopulation', 'totalpop18plus',
        ]]
    )

    cdc_df.to_csv(cdc_path, index = False)

### Load in asthma data
cdc_df = pd.read_csv(cdc_path)

### Preview asthma data
cdc_df

# Change tract identifier datatype for merging
cdc_df["tract"] = cdc_df["tract"].astype(str)
chi_tract_gdf["tract2010"] = chi_tract_gdf["tract2010"].astype(str)

# Merge census data with geometry
tract_cdc_gdf = (
    chi_tract_gdf.merge(
        cdc_df,
        left_on = 'tract2010',
        right_on = 'tract',
        how = 'inner'           # Only keep tracts with asthma data
    )
    [['tract2010', 'asthma', 'asthma_ci_low', 'asthma_ci_high', 'geometry',]]
)

tract_cdc_gdf

### Plot asthma data as chloropleth
asthma_plot = (
    gv.tile_sources.EsriImagery
    *
    gv.Polygons(
        tract_cdc_gdf.to_crs(ccrs.Mercator()),
        vdims = ['asthma', 'tract2010'],
        crs = ccrs.Mercator()

    ).opts(color = 'asthma', colorbar = True, tools = ['hover'])
).opts(width = 600, height = 600, xaxis = None, yaxis = None)

asthma_plot

# Census API Key
income_API_key = '87f7d00c90e94cc038e9714efd302a96d6d49803'

# Set up a path for the income data
income_path = os.path.join(dir, 'income.csv')

# Download income data (only once)
if not os.path.exists(income_path):
    income_url = "https://api.census.gov/data/2023/acs/acs5" # Income only tracked on ACS 5-Year Census data 
    parameters = {
        "get": "B19013_001E,B19301_001E", # 'get' median household income and per-capita income respectively
        "for": "tract:*",                 # one row per census tract
        "in": "state:17 county:031",       # 'in' Cook County, Illinois
        "key": income_API_key
    }
    
    # Make the API request
    response = requests.get(income_url, params = parameters)
    income_data = response.json()

    # Convert to DF
    income_df = pd.DataFrame(
        income_data[1:],
        columns = income_data[0]
    )
    
    # # Progress check
    # print(income_df.head())

    income_df = income_df.rename(columns={
    "B19013_001E": "median_household_income",
    "B19301_001E": "per_capita_income"
    })
    
    # Convert income columns to numeric
    income_df["median_household_income"] = pd.to_numeric(
    income_df["median_household_income"], errors="coerce")
    
    income_df["per_capita_income"] = pd.to_numeric(
    income_df["per_capita_income"], errors="coerce")

    # Create tractID column for merging
    income_df["tractID"] = income_df["state"] + income_df["county"] + income_df["tract"]

    # # Progress check
    # print(income_df.head())

# Save to CSV
else:
    income_df = pd.read_csv(income_path)
   

income_df

# Change tract identifier datatype for merging
income_df["tractID"] = income_df["tractID"].astype(str)


# Combine income data with existing tract + asthma data
inc_tract_df = (
    income_df.merge(
        tract_cdc_gdf, 
        left_on = "tractID", 
        right_on = "tract2010",
        how = "inner"  # Only keep tracts with full data
    )
    [['tractID', 'asthma', 'asthma_ci_low', 'asthma_ci_high', 'median_household_income', 'per_capita_income', 'geometry',]]

)
inc_tract_df

# Convert to GeoDataFrame
inc_tract_gdf = gpd.GeoDataFrame(
    inc_tract_df,
    geometry='geometry',
    crs=chi_tract_gdf.crs  # use the original CRS from your tract GDF
)

### Plot income data as chloropleth
pc_inc_plot = (
    gv.tile_sources.EsriImagery
    *
    gv.Polygons(
        inc_tract_gdf.to_crs(ccrs.Mercator()),
        vdims = ['per_capita_income', 'tractID'],
        crs = ccrs.Mercator()

    ).opts(color = 'per_capita_income', colorbar = True, tools = ['hover'],
           colorbar_opts = {'formatter': NumeralTickFormatter(format="$0,0")})      # Format colorbar as currency
).opts(width = 600, height = 600, xaxis = None, yaxis = None)

pc_inc_plot

### Plot median income data as chloropleth
med_inc_plot = (
    gv.tile_sources.EsriImagery
    *
    gv.Polygons(
        inc_tract_gdf.to_crs(ccrs.Mercator()),
        vdims = ['median_household_income', 'tractID'],
        crs = ccrs.Mercator()

    ).opts(color = 'median_household_income', colorbar = True, tools = ['hover'],
           colorbar_opts = {'formatter': NumeralTickFormatter(format="$0,0")})      # Format colorbar as currency
).opts(width = 600, height = 600, xaxis = None, yaxis = None)

med_inc_plot

# Replace extreme negative outliers with NaN
inc_tract_gdf['median_household_income'] = inc_tract_gdf['median_household_income'].replace({-666666666: np.nan})
inc_tract_gdf['per_capita_income'] = inc_tract_gdf['per_capita_income'].replace({-666666666: np.nan})

### Plot median income data as chloropleth
med_inc_plot = (
    gv.tile_sources.EsriImagery
    *
    gv.Polygons(
        inc_tract_gdf.to_crs(ccrs.Mercator()),
        vdims = ['median_household_income', 'tractID'],
        crs = ccrs.Mercator()

    ).opts(color = 'median_household_income', colorbar = True, tools = ['hover'],
           colorbar_opts = {'formatter': NumeralTickFormatter(format="$0,0")})      # Format colorbar as currency
).opts(width = 600, height = 600, xaxis = None, yaxis = None)

med_inc_plot

### Connect to the planetary computer catalog
e84_catalog = pystac_client.Client.open(
    "https://planetarycomputer.microsoft.com/api/stac/v1"
)

# ONLY RUN ONCE TO DOWNLOAD DATA

### Convert geometry to lat/lon for STAC
tract_latlong_gdf = inc_tract_gdf.to_crs(epsg = 4326)

### Define a path to save NDVI stats
ndvi_stats_path = os.path.join(dir, 'chicago-ndvi-stats.csv')

### Check for existing data - do not access duplicate tracts
downloaded_tracts = []

if os.path.exists(ndvi_stats_path):
    ndvi_stats_df = pd.read_csv(ndvi_stats_path)

    downloaded_tracts = ndvi_stats_df.tract.values
else:
    print("No census tracts downloaded yet.")

### Loop through each census tract

scene_dfs = []


for i, tract_values in tqdm(tract_latlong_gdf.iterrows()):

    tract = tract_values.tractID
    
    ### Check if statistics are already downloaded for this tract
    if not (tract in downloaded_tracts):
      
        ### Repeat up to 5 times in case of a momentary disruption 
        i = 0
        retry_limit = 5
        while i < retry_limit:

            ### Try accessing the STAC
            try:

                ### Search for tiles 
                naip_search = e84_catalog.search(
                    collections = ['naip'],

                    intersects = shapely.to_geojson(tract_values.geometry),
                    datetime="2021"
                )

                ### Build dataframe with tracts and tile urls
                scene_dfs.append(pd.DataFrame(dict(

                    tract = tract,
                    date = [pd.to_datetime(scene.datetime).date()
                            
                            for scene in naip_search.items()],

                    rgbir_href = [scene.assets['image'].href for scene in naip_search.items()]
                )))
                break

            ### Try again in case of an APIError
            except pystac_client.exceptions.APIError:
                print(
                    f"Could not connect to STAC for tract {tract}. "
                    f"Retrying tract {tract}..."
                )
                time.sleep(2)
                i+=1
                continue

### Concatenate the url dataframes
if scene_dfs:
    scene_df = pd.concat(scene_dfs).reset_index(drop = True)
else:
    scene_df = None

### Preview the url dataframe
scene_df

# Save to csv, will only work when downloading data for the first time

scene_df.to_csv(ndvi_stats_path, index = False)

# make csv for streaming ndvi data, has to be run each time to set the path

ndvi_stats_path_veg = os.path.join(dir, 'chicago-ndvi-veg-test.csv')

# ONLY RUN ONCE TO DOWNLOAD DATA

downloaded_tracts = []

if os.path.exists(ndvi_stats_path):
    ndvi_stats_df = pd.read_csv(ndvi_stats_path)
    downloaded_tracts = ndvi_stats_df.tract.values  # already processed tracts

# Filter scene_df to only tracts that haven't been processed
if scene_df is not None:
    scene_df_to_process = scene_df[~scene_df['tract'].isin(downloaded_tracts)]
else:
    scene_df_to_process = None


# Full loop for all tracts
if scene_df_to_process is not None and len(scene_df_to_process) > 0:

    ### Loop through the census tracts with URLs
    for tract, tract_date_gdf in tqdm(scene_df_to_process.groupby('tract')):
        
        ### Open all images for tract
        tile_das = []
        
        # loop through each scene for this tract
        for _, href_s in tract_date_gdf.iterrows():
            
            ### Open vsi connection to data
            tile_da = rxr.open_rasterio(

                # location of the raster image
                href_s.rgbir_href,

                # deal with no data, remove extra dimensions
                masked = True).squeeze()

            ### Clip data
            boundary = (
                inc_tract_gdf

                # deal with integer issues
                .assign(tractID = lambda df: df["tractID"].astype(str))

                # use tract ID as index   
                .set_index('tractID')

                # select the geometry for this tract
                .loc[[str(tract)]]

                #reproject to match the tile CRS
                .to_crs(tile_da.rio.crs)

                #extract the geometry
                .geometry)
            
            ### Crop to bounding box
            crop_da = tile_da.rio.clip_box(
                *boundary.envelope.total_bounds,
                auto_expand = True)
            
            ### Clip data to the boundary of the census tract
            clip_da = crop_da.rio.clip(
                boundary,
                all_touched = True) 

            ### Compute NDVI
            ndvi_da = (
                (clip_da.sel(band = 4) - clip_da.sel(band = 1)) /
                (clip_da.sel(band = 4) + clip_da.sel(band = 1))
            )

            ### Accumulate result
            tile_das.append(ndvi_da)

        ### Merge data
        scene_da = rxrm.merge_arrays(tile_das)

        ### Mask vegetation
        veg_mask = (scene_da > 0.3)

        ### Calculate statistics and save data to file

        # count all valid pixels
        total_pixels = scene_da.notnull().sum()

        # count all vegetated pixels
        veg_pixels = veg_mask.sum()

        ### identify vegetation patches
        labeled_patches, num_patches = label(veg_mask)

        # count patch pixels
        patch_sizes = np.bincount(labeled_patches.ravel())[1:]

        ### Calculate mean patch size
        mean_patch_size = patch_sizes.mean()

        ### Calculate edge density
        
        ### Make kernel to calculate edge density
        kernel = np.array([
            [1, 1, 1], 
            [1, -8, 1], 
            [1, 1, 1]])

        ### detect boundaries
        edges = convolve(veg_mask, kernel, mode='constant')
        
        # calculate edge density
        edge_density = np.sum(edges != 0) / veg_mask.size
        
        ### Add a row to the statistics file for this tract
        # create a dataframe for this tract
        pd.DataFrame(dict(

            #store tract ID
            tract = [tract],

            #store total pixels
            total_pixels = [int(total_pixels)],
            
            #store fraction of vegetated pixels
            fract_veg = [float(veg_pixels/total_pixels)],

            #store mean patch size
            mean_patch_size = [mean_patch_size],
            
            #store edge density
            edge_density = [edge_density]

        # write out as csv and save
        )).to_csv(
            ndvi_stats_path_veg,

            #append mode
            mode = 'a',

            # get rid of row numbers
            index = False,

            # write header only if file does not already exist
            header = (not os.path.exists(ndvi_stats_path_veg))           
        )

# check the file is loading correctly
# Save to CSV
ndvi_stats_df = pd.read_csv(ndvi_stats_path_veg)

ndvi_stats_df

# Change tract identifier datatype for merging
ndvi_stats_df["tract"] = ndvi_stats_df["tract"].astype(str)

# Add NDVI statistics to existing dataframe
ndvi_inc_gdf = (
    inc_tract_gdf.merge(
        ndvi_stats_df,
        left_on = 'tractID',
        right_on = 'tract',
        how = 'inner'           # Only keep tracts with NDVI data
    )
)

ndvi_inc_gdf.head()

fract_veg_plot = (
    gv.tile_sources.EsriImagery
    *
    gv.Polygons(
        ndvi_inc_gdf.to_crs(ccrs.Mercator()),
        vdims = ['fract_veg', 'tractID'],
        crs = ccrs.Mercator()

    ).opts(color = 'fract_veg', colorbar = True, tools = ['hover'])
).opts(width = 600, height = 600, xaxis = None, yaxis = None)

fract_veg_plot

mean_veg_plot = (
    gv.tile_sources.EsriImagery
    *
    gv.Polygons(
        ndvi_inc_gdf.to_crs(ccrs.Mercator()),
        vdims = ['mean_patch_size', 'tractID'],
        crs = ccrs.Mercator()

    ).opts(color = 'mean_patch_size', colorbar = True, tools = ['hover'])
).opts(width = 600, height = 600, xaxis = None, yaxis = None)

mean_veg_plot

### Visualize distribution of data

# graph for variables
vars = ['fract_veg', 'edge_density', 'mean_patch_size', 
        'per_capita_income','median_household_income','asthma']

# scatter plot matrix
pd.plotting.scatter_matrix(
    ndvi_inc_gdf[vars],
    figsize = (10, 10)
)

array([[<Axes: xlabel='fract_veg', ylabel='fract_veg'>,
        <Axes: xlabel='edge_density', ylabel='fract_veg'>,
        <Axes: xlabel='mean_patch_size', ylabel='fract_veg'>,
        <Axes: xlabel='per_capita_income', ylabel='fract_veg'>,
        <Axes: xlabel='median_household_income', ylabel='fract_veg'>,
        <Axes: xlabel='asthma', ylabel='fract_veg'>],
       [<Axes: xlabel='fract_veg', ylabel='edge_density'>,
        <Axes: xlabel='edge_density', ylabel='edge_density'>,
        <Axes: xlabel='mean_patch_size', ylabel='edge_density'>,
        <Axes: xlabel='per_capita_income', ylabel='edge_density'>,
        <Axes: xlabel='median_household_income', ylabel='edge_density'>,
        <Axes: xlabel='asthma', ylabel='edge_density'>],
       [<Axes: xlabel='fract_veg', ylabel='mean_patch_size'>,
        <Axes: xlabel='edge_density', ylabel='mean_patch_size'>,
        <Axes: xlabel='mean_patch_size', ylabel='mean_patch_size'>,
        <Axes: xlabel='per_capita_income', ylabel='mean_patch_size'>,
        <Axes: xlabel='median_household_income', ylabel='mean_patch_size'>,
        <Axes: xlabel='asthma', ylabel='mean_patch_size'>],
       [<Axes: xlabel='fract_veg', ylabel='per_capita_income'>,
        <Axes: xlabel='edge_density', ylabel='per_capita_income'>,
        <Axes: xlabel='mean_patch_size', ylabel='per_capita_income'>,
        <Axes: xlabel='per_capita_income', ylabel='per_capita_income'>,
        <Axes: xlabel='median_household_income', ylabel='per_capita_income'>,
        <Axes: xlabel='asthma', ylabel='per_capita_income'>],
       [<Axes: xlabel='fract_veg', ylabel='median_household_income'>,
        <Axes: xlabel='edge_density', ylabel='median_household_income'>,
        <Axes: xlabel='mean_patch_size', ylabel='median_household_income'>,
        <Axes: xlabel='per_capita_income', ylabel='median_household_income'>,
        <Axes: xlabel='median_household_income', ylabel='median_household_income'>,
        <Axes: xlabel='asthma', ylabel='median_household_income'>],
       [<Axes: xlabel='fract_veg', ylabel='asthma'>,
        <Axes: xlabel='edge_density', ylabel='asthma'>,
        <Axes: xlabel='mean_patch_size', ylabel='asthma'>,
        <Axes: xlabel='per_capita_income', ylabel='asthma'>,
        <Axes: xlabel='median_household_income', ylabel='asthma'>,
        <Axes: xlabel='asthma', ylabel='asthma'>]], dtype=object)

# drop missing data

model_gdf = (
    ndvi_inc_gdf
    
    #make a copy to avoid modifying original data
    .copy()

    # subset to columns
    [['tractID','fract_veg', 'edge_density', 'mean_patch_size', 
        'per_capita_income','median_household_income','asthma', 'geometry']]

    # drop NA
    .dropna()
)

model_gdf

# Calculate logs
for col in ['fract_veg', 'edge_density', 'mean_patch_size', 
            'per_capita_income','median_household_income','asthma']:
    model_gdf[f'log_{col}'] = np.log(model_gdf[col])

model_gdf

# q-q plots

# set variables for q-q plots
var_qq = [
    'fract_veg', 'log_fract_veg', 'edge_density', 'log_edge_density', 'mean_patch_size', 'log_mean_patch_size', 
    'per_capita_income','log_per_capita_income','median_household_income','log_median_household_income','asthma','log_asthma'
]

# make plot for each variable
plt.figure(figsize = (12,10))
for i, var in enumerate(var_qq, 1):
    
    # 2x2 facet
    plt.subplot(6, 2, i)

    # norm distribution q-q plot
    stats.probplot(model_gdf[var], dist="norm", plot=plt)

    # add title
    plt.title(f'Q-Q Plot of {var}')

plt.tight_layout()
plt.show()

# Set predictor and response variables for modeling
X = model_gdf[['log_fract_veg', 'log_mean_patch_size', 'log_median_household_income']]
Y = model_gdf[['log_asthma']]

# Split data into training and testing sets
X_train, X_test, Y_train, Y_test = train_test_split(
    X, Y, test_size=0.33, random_state=42
)

# Fit linear regression model
reg = LinearRegression()
reg.fit(X_train, Y_train)   

# Make predictions on the test set
Y_test['pred_asthma'] = np.exp(reg.predict(X_test))

# use the trained model to predict asthma for all tracts
model_gdf['pred_asthma'] = np.exp(reg.predict(X))

Y_test['measured_asthma'] = np.exp(Y_test['log_asthma'])

Y_test

# vmin = Y_test[cols].min().min()
# vmax = Y_test[cols].max().max()

p_est = (Y_test
    .hvplot.scatter(x='measured_asthma', y='pred_asthma',
                    xlabel = 'Measured Asthma Prevalence',
                    ylabel = 'Predicted Asthma Prevalence',
                    title = 'Regression Model Distribution')
    .opts(aspect='equal', 
        #   xlim=(xylim), ylim=(xylim), 
          width=600, height=600)
) * hv.Slope(slope=1, y_intercept=0).opts(color='black')

p_est

model_gdf = gpd.GeoDataFrame(
    model_gdf,
    geometry='geometry',
    crs=ndvi_inc_gdf.crs  # use the original CRS
)

model_gdf

# Calculate error 
model_gdf['error_asthma'] = model_gdf['pred_asthma'] - model_gdf['asthma']

# Set limit
abs_max = model_gdf['error_asthma'].abs().max()
clim = (-abs_max, abs_max)


# Plot error
model_plot = (
    gv.tile_sources.EsriImagery
    *
    gv.Polygons(
        model_gdf.to_crs(ccrs.Mercator()),
        vdims=['error_asthma', 'pred_asthma', 'asthma', 'tractID'],
        crs = ccrs.Mercator()    
    ).opts(color = 'error_asthma', colorbar = True, tools = ['hover'],
           clim = clim, cmap = 'RdBu'  # Diverging color map)
).opts(width = 600, height = 600, xaxis = None, yaxis = None, title = 'Asthma Prediction Error for Chicago, IL Census Tracts',
       clabel = 'Lower values indicate under-prediction, higher values indicate over-prediction')
)
model_plot

y_true = model_gdf['asthma'].values       # observed
y_pred = model_gdf['pred_asthma'].values  # predicted

# Example if you know which rows were training/testing
train_mask = model_gdf.index.isin(X_train.index)
test_mask  = model_gdf.index.isin(X_test.index)

r2_train = r2_score(y_true[train_mask], y_pred[train_mask])
r2_test  = r2_score(y_true[test_mask], y_pred[test_mask])

print(f"Training R²: {r2_train:.3f}")
print(f"Test R²: {r2_test:.3f}")

Training R²: 0.522
Test R²: 0.584

# Calculate R² for all data
r2 = r2_score(y_true, y_pred)
print(f"R² (all): {r2:.3f}")

R² (all): 0.546

# Calculate R² for training and test sets
train_mask = model_gdf.index.isin(X_train.index)
test_mask  = model_gdf.index.isin(X_test.index)

r2_train = r2_score(y_true[train_mask], y_pred[train_mask])
r2_test  = r2_score(y_true[test_mask], y_pred[test_mask])

print(f"Training R²: {r2_train:.3f}")
print(f"Test R²: {r2_test:.3f}")

Training R²: 0.522
Test R²: 0.584

descriptor_text = (
    f"Model performance summary:\n"
    f"Using log_fract_veg, log_mean_patch_size, and log_mean_household_income, \n"
    f"this model estimates asthma against predicted asthma with R² = {r2:.3f}."
)

text_panel = hv.Text(
    0.5, 0.5, descriptor_text
).opts(
    width=600,
    height=120,
    xaxis=None,
    yaxis=None,
    text_align='center',
    text_baseline='middle',
    text_font_size='10pt'
)

final_plot = (model_plot + text_panel).cols(1)
final_plot

# save final plot
hv.save(final_plot, 'img/descrip_asthma_error_map.html', fmt='html')

	place2010	tract2010	ST	PlaceName	plctract10	PlcTrPop10	geometry
0	1714000	17031010100	17	Chicago	1714000-17031010100	4854	POLYGON ((-9758835.381 5164429.383, -9758837.3...
1	1714000	17031010201	17	Chicago	1714000-17031010201	6450	POLYGON ((-9760143.496 5163888.741, -9760143.4...
2	1714000	17031010202	17	Chicago	1714000-17031010202	2818	POLYGON ((-9759754.212 5163883.196, -9759726.6...
3	1714000	17031010300	17	Chicago	1714000-17031010300	6236	POLYGON ((-9758695.229 5163870.91, -9758695.78...
4	1714000	17031010400	17	Chicago	1714000-17031010400	5042	POLYGON ((-9757724.634 5160715.939, -9757742.2...
...	...	...	...	...	...	...	...
804	1714000	17031835700	17	Chicago	1714000-17031835700	0	POLYGON ((-9754496.811 5132719.307, -9754491.8...
805	1714000	17031980000	17	Chicago	1714000-17031980000	0	POLYGON ((-9788665.342 5161808.277, -9788667.6...
806	1714000	17031980100	17	Chicago	1714000-17031980100	0	POLYGON ((-9766922.964 5128945.613, -9766938.5...
807	1714000	17043840000	17	Chicago	1714000-17043840000	0	POLYGON ((-9787210.28 5154713.902, -9787240.67...
808	1714000	17043840801	17	Chicago	1714000-17043840801	0	POLYGON ((-9787431.695 5154736.805, -9787441.0...

	year	tract	asthma	asthma_ci_low	asthma_ci_high	data_value_unit	totalpopulation	totalpop18plus
0	2023	17031071700	9.1	8.1	10.1	%	1660	1325
1	2023	17031120300	8.8	7.8	9.8	%	6920	5212
2	2023	17031010501	9.9	8.9	11.0	%	4206	3762
3	2023	17031031000	8.9	7.9	9.9	%	3868	3439
4	2023	17031062400	9.2	8.2	10.3	%	1673	1389
...	...	...	...	...	...	...	...	...
1323	2023	17031840400	7.9	7.1	8.8	%	3369	2662
1324	2023	17031837300	13.7	12.3	15.0	%	2489	1835
1325	2023	17031840000	8.4	7.5	9.3	%	3001	2428
1326	2023	17031840700	8.3	7.3	9.2	%	3900	2885
1327	2023	17031838700	14.9	13.3	16.6	%	4132	2874

	tract2010	asthma	asthma_ci_low	asthma_ci_high	geometry
0	17031010100	11.3	10.1	12.5	POLYGON ((-9758835.381 5164429.383, -9758837.3...
1	17031010201	11.2	10.0	12.4	POLYGON ((-9760143.496 5163888.741, -9760143.4...
2	17031010202	10.2	9.1	11.3	POLYGON ((-9759754.212 5163883.196, -9759726.6...
3	17031010300	10.2	9.1	11.3	POLYGON ((-9758695.229 5163870.91, -9758695.78...
4	17031010400	10.6	9.5	11.7	POLYGON ((-9757724.634 5160715.939, -9757742.2...
...	...	...	...	...	...
783	17031770700	9.7	8.6	10.8	POLYGON ((-9780753.304 5157066.079, -9780752.0...
784	17031770800	9.5	8.4	10.6	POLYGON ((-9783235.84 5154620.343, -9783211.23...
785	17031805600	9.1	8.1	10.1	POLYGON ((-9776210.02 5161605.738, -9776213.47...
786	17031807900	8.5	7.5	9.4	POLYGON ((-9768609.902 5160576.634, -9768654.5...
787	17031808100	9.2	8.1	10.3	MULTIPOLYGON (((-9774480.671 5161127.722, -977...

	tractID	asthma	asthma_ci_low	asthma_ci_high	median_household_income	per_capita_income	geometry
0	17031010100	11.3	10.1	12.5	69460	45353	POLYGON ((-9758835.381 5164429.383, -9758837.3...
1	17031010201	11.2	10.0	12.4	49639	31978	POLYGON ((-9760143.496 5163888.741, -9760143.4...
2	17031010202	10.2	9.1	11.3	55119	33488	POLYGON ((-9759754.212 5163883.196, -9759726.6...
3	17031010300	10.2	9.1	11.3	65871	42487	POLYGON ((-9758695.229 5163870.91, -9758695.78...
4	17031010400	10.6	9.5	11.7	49017	33185	POLYGON ((-9757724.634 5160715.939, -9757742.2...
...	...	...	...	...	...	...	...
783	17031843500	9.5	8.3	10.7	55833	3546	POLYGON ((-9761322.813 5136241.389, -9761337.5...
784	17031843600	12.5	11.2	14.0	71359	38837	POLYGON ((-9752318.844 5132492.145, -9752318.2...
785	17031843700	8.9	7.9	9.9	134000	101400	POLYGON ((-9761412.872 5153004.52, -9761411.75...
786	17031843800	10.9	9.7	12.0	57885	27767	POLYGON ((-9755524.513 5130243.96, -9755529.18...
787	17031843900	13.1	11.7	14.7	47760	34298	POLYGON ((-9748410.585 5128192.165, -9748480.7...

	tract	total_pixels	fract_veg	mean_patch_size	edge_density
0	17031010100	1059033	0.178657	55.225919	0.118612
1	17031010201	1531554	0.213859	57.543394	0.161668
2	17031010202	978546	0.186055	63.260250	0.123673
3	17031010300	1308392	0.191675	57.113642	0.126384
4	17031010400	1516964	0.198563	52.983817	0.079474
...	...	...	...	...	...
783	17031843500	5647650	0.075254	9.732779	0.104686
784	17031843600	1142916	0.054393	9.177296	0.101217
785	17031843700	6025768	0.027644	7.477533	0.047642
786	17031843800	3639014	0.093920	24.169295	0.105052
787	17031843900	4521964	0.199113	23.985215	0.124282

Set-Up¶

This code is a workflow expanding on previous work with Chicago census tracts and NDVI data. I am focussed on implementing income data and evaluating/refining the performance of the model.¶

Access income data and add to the GDF¶

NDVI Data¶

Run Regression¶

R² Calculation¶

	median_household_income	per_capita_income	state	county	tract	tractID
0	69460	45353	17	31	10100	17031010100
1	49639	31978	17	31	10201	17031010201
2	55119	33488	17	31	10202	17031010202
3	65871	42487	17	31	10300	17031010300
4	49017	33185	17	31	10400	17031010400
...	...	...	...	...	...	...
1327	56848	29766	17	31	844600	17031844600
1328	69583	27809	17	31	844700	17031844700
1329	-666666666	-666666666	17	31	980000	17031980000
1330	-666666666	-666666666	17	31	980100	17031980100
1331	-666666666	-666666666	17	31	990000	17031990000

	log_asthma	pred_asthma	measured_asthma
574	2.332144	11.898119	10.3
535	2.091864	10.189445	8.1
616	2.602690	11.847563	13.5
109	2.240710	10.113142	9.4
592	2.493205	12.858251	12.1
...	...	...	...
18	2.151762	9.718228	8.6
576	2.219203	11.059941	9.2
141	2.186051	7.897718	8.9
337	2.617396	11.558575	13.7
260	2.174752	8.782103	8.8

Set-Up¶

This code is a workflow expanding on previous work with Chicago census tracts and NDVI data. I am focussed on implementing income data and evaluating/refining the performance of the model.¶

Access income data and add to the GDF¶

NDVI Data¶

Run Regression¶

R2 Calculation¶

R² Calculation¶